rs10493964

Variant names:

• chr1-102018655-A-G
• rs10493964

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.446 in 152,044 control chromosomes in the GnomAD database, including 15,572 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (15572 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67777 AN: 151926 Hom.: 15572 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.529

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.446 AC: 67796 AN: 152044 Hom.: 15572 Cov.: 32 AF XY: 0.440 AC XY: 32675 AN XY: 74300

African (AFR) AF: 0.385 AC: 15955 AN: 41460

American (AMR) AF: 0.534 AC: 8152 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2135 AN: 3472

East Asian (EAS) AF: 0.569 AC: 2946 AN: 5176

South Asian (SAS) AF: 0.451 AC: 2170 AN: 4816

European-Finnish (FIN) AF: 0.280 AC: 2950 AN: 10554

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31806 AN: 67970

Other (OTH) AF: 0.528 AC: 1116 AN: 2112

Alfa AF: 0.464 Hom.: 9271

Bravo AF: 0.462

Asia WGS AF: 0.509 AC: 1769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.66
PhyloP100		1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10493964; hg19: chr1-102484211;